Minecraft isn't really a property I'm familiar with at all, so while I can't say for sure, I at least feel like you've done a good job of analyzing this story in terms of what is and isn't correct for Minecraft.
I'm having difficulty putting my thoughts about the agents into words. On the one hand, neither one feels like they dominate the narrative or the relationship all the way through, which is good. They both take turns being the leader from scene to scene, and keeping the other's worse impulses in check. On the other hand . . . again, I feel like I'm not phrasing my feelings properly, but it doesn't feel to me like they're quite a team? I get the impression they're working together in order to get the job done, rather than because working together is what they do? But this is all ultimately a first impression, I realize both agents need more appearances to really reveal themselves to us readers. So don't take this is a criticism so much as an observation.
One thing in your analysis I'm not really agreeing with is Herobrine and Aria being related. Unless the fic calls Herobrine and Steve brothers frequently in parts of the story you didn't quote, I really feel like that line from the beginning, when Herobrine calls Steve his "twin" was metaphorical. I think it's pointing out how Steve and Herobrine are sort of two sides of the same coin, with Steve being a creative force and Herobrine a destructive one, and with both overlaying the same character model. That said, our missions do have a long history of interpreting things literally, so I think the mission still stands fine with that detail included.
A couple of small details I really liked were:
1. The book ends of the castle being built and then destroyed in Alex's game.
2. That the removal of Herobrine's mansion is done through means available to regular Minecraft players: a combination of deconstructing parts and using explosives. Very appropriate!
Welcome to doctorlit's list of typos:
"And what is it that you have been working on?" she countered seamlessly as she stepped closer . . .
A minor quibble, but I wouldn't personally use "countered" here, since the agents aren't arguing, just catching either up on their activities.
“Beeper. Stop,” she muttered tiredly, focusing on the immediately-fixable problem.
Since "immediately" ends in "-ly" it doesn't need a hyphen connecting it to the word it's describing. "immediately fixable" is correct here.
Ce’rana, who had somehow managed to get herself a few blocks off the ground, promptly fell off the tree and Alex to the dirt beneath his feet when the world began rocking back and forth . . .
I feel like some words got cut from this sentence, because it's not quite reading clearly to me. Was it meant to be "fell off the tree and bounced off Alex to the dirt beneath his feet"?
. . . when he became loud enough to potentially attract the attention of the nearby potential canon replacements.
Paging the RDR, paging the RDR . . .
He guided her until he was sitting down, then crouched next to her.
I think that's meant to be "she" for Ce'rana?
Ce’nedra turned her face from the thick, green-glowing semi-liquid.
Where did Ce'rana go? (I'm guessing this is the name of a canon Dryad from The Belgariad? The name sounds familiar.)
“I suppose it would depend on your difference of ‘much’,” she conceded.
"Definition."
Ce’rana snorted derisively, closing her eyes and leaned back against a tree of her own . . .
"Leaned" should be "leaning" to match the verb tense of "closing." Another option would be adding a comma after "eyes" which would allow all the verbs to stay as they are now, though I think it reads just a little awkwardly that way.
When he looked down, she flattened her fingers and jabbed them straight into his side.
Aren't they in Minecraft-style disguises right now? Does Ce'rana actually have fingers? Sorry if this one is too silly to have broguht up . . .
The pair listened quietly as Aria recounted her saving of Mille . . .
I think you wanted "Millie" here, since you treated "Mille" as a mini earlier in the story. Especially since it's Aria talking about the character; a Mary Sue wouldn't have been aware of a mini within their narrative.
The Dryad smiled faintly and stuck her arm through, passing though in full when she realized he had done the portal thing right this time, probably.
That should be "through," although I just noticed that also makes "through" appear twice in three words. Maybe the first "through" could be changed to "in"?
—doctorlit apologizes for long it took to write this review; it's been a very sleepy week for him